Aid agencies are warning of an imminent health crisis in Haiti, as the onset of the rainy season brings fears of outbreaks of waterborne diseases in Port-au-Prince's squalid refugee camps.

With up to a million Haitians thought to have lost their homes in the earthquake, and hundreds of thousands still living in 600 squatter settlements around the capital, aid officials warn that the arrival of rain could present them with a further medical crisis after hospitals were initially swamped with patients needing amputations or treatment for crushing injuries. Haiti's rains normally come in February and the prospect of bad weather has aid workers and homeless people scared. The hurricane season starts in July.

"If it rains, there will be a great deal of disease," said Dr Thierry Causse, a GP from the French Red Cross who is working at a field clinic near the Place St Pierre refugee camp in Pétionville, where rivers of urine flow through the square.

"We are afraid of a typhoid epidemic, of a malaria epidemic. We have a lot of doctors here, but if there is an epidemic there will be a big problem. There could be a lot of dead people if it is not treated quickly and properly."

One of the largest refugee camps is in the city's football stadium, the Stade Sylvio Cator. On the pitch, thousands of homeless people have made shelters from tarpaulin, corrugated iron and rubble scavenged from fallen buildings. One family is living inside the cramped team dugout where Brazilian football stars such as Ronaldo once sat.

"Where I lived is all gone," said Benita Saint-Cyr, 37, one of three women living in the dugout with dozens of children. "I'm not dead, so all I can do now is pray."

Thervius Luckner, a community leader in the Place St Pierre camp, is also among the city's displaced population. "It always rains in February," he said. "I think it is only because of God that it hasn't rained so far. If it rains, people will be in trouble, the tents are not safe and some people don't even have tents. I got a message from a Haitian doctor to tell the people not to piss and shit in the camp because the kids will get sick."

The UN and the Haitian government say they are planning to move many of Port-au-Prince's homeless to camps outside the city, partly to avert risks of a serious epidemic, but in Place St Pierre such promises have yet to materialise.

"We had an announcement from the mayor saying they were building houses for people whose homes were destroyed," said Luckner. "They took people's names, but we haven't heard anything yet."

Around Luckner's shelter, a tiny cubicle made out of a black tarpaulin donated by a Buddhist relief group from Taiwan, live some of the people most at risk: mothers and their children, who spend the days playing in the filthy square.

"The doctors haven't come yet," said Yolene Philemond, 22, mother of a one-year-old son, when asked if any doctors had visited offering immunisation jabs. "We hope they are coming."

She pointed to a rash on her baby's arms. "He's infected. His body is cracked. I don't know what it is," said Philemond, whose house was levelled by the quake, killing one of her cousins.

"When there is a population displacement and lack of water and sanitation facilities, there is always a risk of diarrhoeal diseases, including cholera," said Roshan Khadivi of Unicef, adding that water and sanitation diseases were major killers of children under five. On Friday Unicef announced a "major immunisation campaign" for the city's children, after reports of measles among the young. Khadivi said the campaign against measles, diphtheria and tetanus would begin on Tuesday.

But aid agencies fear that unless these refugees are properly and rapidly re-housed in government and UN camps outside the city, waterborne diseases could easily proliferate in the squatter settlements, where the stench of raw sewage hangs in the air.

"They are sleeping in the street, peeing in the street and shitting in the street. Their parents are sad because they have lost children, friends or family members," said Pierre Biales, a Paris-based psychologist from the Red Cross, who is offering counselling and trying to teach basic hygiene to children in the camps. "Taking care of the children is now an emergency."